The performance of MODIS-Aqua Chl-a derived from the standard OC3 band-ratio algorithm and a new band-difference OCI algorithm are compared in the South China Sea(SCS) from the MODIS instrument on the Aqua satellite with nine cruises of chlorophyll measurements collected from 2004 to 2012. Then, the algorithms of OC3 and OCI were corrected by the parameter adjustments based on the satellite, in situ remote sensing reflectance (Rrs(λ)) and corresponding in situ Chl-a pairs respectively. The results show that MODIS-Aqua Chl-a products derived from OC3 and OCI algorithms overestimate the in situ data, with the Average Relative Error(APD) of 59.41% and 44 17%, respectively. However, the algorithm OCI significantly improves the retrieval accuracy for low chlorophyll concentration waters(<0.25 mg·m-3). After regional correction by MODIS-Aqua Rrs(λ) and corresponding Chl-a pairs, the algorithms are likely to fare better, and the modified algorithm NOC3 and NOCI show their APD accuracies are 37.85% and 36.74%, respectively. Moreover, the algorithms NOC3 and NOCI modified by in situ Rrs(λ) and corresponding Chl-a pairs also give a good estimateion with the APD accuracy of 36.61% and 37.79%. Therefore, it suggests that to conduct the regional correction for the operational algorithms is important to improve the accuracy of Chl-a estimation in the SCS.